Buggy code:
public class GeneParser extends CellBaseParser { private Map < String , Integer > transcriptDict ; private Map < String , Exon > exonDict ; private Path gtfFile ; private Path proteinFastaFile ; private Path cDnaFastaFile ; private Path geneDescriptionFile ; private Path xrefsFile ; private Path uniprotIdMappingFile ; private Path tfbsFile ; private Path mirnaFile ; private Path genomeSequenceFilePath ; private Connection sqlConn ; private PreparedStatement sqlQuery ; private int CHUNK_SIZE = 2000 ; private String chunkIdSuffix = ( ( CHUNK_SIZE ) // 1000 ) + "k" ; public GeneParser ( Path geneDirectoryPath , Path genomeSequenceFastaFile , CellBaseSerializer serializer ) { } public GeneParser ( Path gtfFile , Path geneDescriptionFile , Path xrefsFile , Path uniprotIdMappingFile , Path tfbsFile , Path mirnaFile , Path genomeSequenceFilePath , CellBaseSerializer serializer ) { } public void parse ( ) throws IOException , InterruptedException , NoSuchMethodException , SecurityException , FileFormatException { } private ArrayList < TranscriptTfbs > getTranscriptTfbses ( Gtf transcript , String chromosome , Map < String , SortedSet < Gff2 > > tfbsMap ) { } private ArrayList < TranscriptTfbs > addTranscriptTfbstoList ( Gff2 tfbs , Gtf transcript , String chromosome , ArrayList < TranscriptTfbs > transcriptTfbses ) { } private Integer getRelativeTranscriptTfbsStart ( Gff2 tfbs , Gtf transcript ) { } private Integer getRelativeTranscriptTfbsEnd ( Gff2 tfbs , Gtf transcript ) { Integer relativeEnd ; if ( transcript . getStrand ( ) . equals ( "+" ) ) { if ( ( tfbs . getEnd ( ) ) < ( transcript . getStart ( ) ) ) { relativeEnd = ( tfbs . getEnd ( ) ) - ( transcript . getStart ( ) ) ; } else { relativeEnd = ( ( tfbs . getEnd ( ) ) - ( transcript . getStart ( ) ) ) + 1 ; } } else { if ( ( tfbs . getStart ( ) ) > ( transcript . getEnd ( ) ) ) { relativeEnd = ( transcript . getEnd ( ) ) - ( tfbs . getStart ( ) ) ; } else { <START_BUG> relativeEnd = ( ( transcript . getEnd ( ) ) - ( tfbs . getEnd ( ) ) ) + 1 ; <END_BUG> } } return relativeEnd ; } private Map < String , SortedSet < Gff2 > > getTfbsMap ( ) { } private void addTfbsMotifToMap ( Map < String , SortedSet < Gff2 > > tfbsMap , Gff2 tfbsMotifFeature ) { } private Map < String , Fasta > getCDnaSequencesMap ( ) throws IOException , FileFormatException { } private Map < String , Fasta > getProteinSequencesMap ( ) throws IOException , FileFormatException { } private Map < String , ArrayList < Xref > > getXrefMap ( ) throws IOException { } private Map < String , String > getGeneDescriptionMap ( ) throws IOException { } private boolean newGene ( Gene previousGene , String newGeneId ) { } private void connect ( Path genomeSequenceFilePath ) throws IOException , ClassNotFoundException , SQLException { } private void disconnectSqlite ( ) throws SQLException { } private void indexReferenceGenomeFasta ( Path genomeSequenceFilePath ) throws IOException , ClassNotFoundException , SQLException { } private void insertGenomeSequence ( String sequenceName , boolean haplotypeSequenceType , PreparedStatement sqlInsert , StringBuilder sequenceStringBuilder ) throws SQLException { } private String getExonSequence ( String sequenceName , int start , int end ) throws SQLException { } private int getChunk ( int position ) { } private int getOffset ( int position ) { } private void updateTranscriptAndGeneCoords ( Transcript transcript , Gene gene , Gtf gtf ) { } private Map < String , MiRNAGene > getmiRNAGeneMap ( Path mirnaGeneFile ) throws IOException { } private void getGtfFileFromGeneDirectoryPath ( Path geneDirectoryPath ) { } private void getProteinFastaFileFromGeneDirectoryPath ( Path geneDirectoryPath ) { } private void getCDnaFastaFileFromGeneDirectoryPath ( Path geneDirectoryPath ) { } }

Fix:
relativeEnd = ( ( transcript . getEnd ( ) ) - ( tfbs . getStart ( ) ) ) + 1 ;